6DUB: Methyltransferase

Name: PDB 6DUB: Crystal structure of a methyltransferase
Published: 2018-07-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of a methyltransferase. Determined by X-ray diffraction at 1.2 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,160
Mol. weight: 52.43 kDa
Ligands: SAH
Released: 25 Jul 2018

Explore 6DUB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DUB contains 29 α-helices and 25 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
α-helix	83-86	4
α-helix	91-93	3
α-helix	94-105	12
β-strand	109	1	1
β-strand	115	1	1
β-strand	119-123	5	2
α-helix	129-130	2
α-helix	131-135	5
β-strand	141-146	6	2
α-helix	149-158	10
α-helix	160-165	6
β-strand	166-171	6	2
α-helix	174-176	3
α-helix	179-180	2
β-strand	184-190	7	2
α-helix	193-195	3
α-helix	198-210	13
β-strand	212-223	12	2
β-strand	224-225	2	3
β-strand	229-232	4	3
β-strand	237-241	5	3
α-helix	242-251	10
β-strand	256-261	6	2
α-helix	262-263	2
α-helix	270-271	2
β-strand	272-277	6	2

Chain B: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
α-helix	83-86	4
α-helix	91-93	3
α-helix	94-108	15
β-strand	109	1	4
β-strand	115	1	4
β-strand	119-123	5	5
α-helix	129-130	2
α-helix	131-135	5
β-strand	141-146	6	5
α-helix	149-158	10
α-helix	160-165	6
β-strand	166-171	6	5
α-helix	174-176	3
β-strand	184-190	7	5
α-helix	193-195	3
α-helix	198-210	13
β-strand	212-223	12	5
β-strand	225	1	6
β-strand	230-232	3	7
β-strand	237-239	3	7
β-strand	241	1	6
α-helix	242-251	10
β-strand	256-261	6	5
α-helix	262-263	2
α-helix	270-271	2
β-strand	272-277	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha N-terminal protein methyltransferase 1B	A, B	protein	222	Homo sapiens	Q5VVY1 (AlphaFold model)
RCC1	E, F	protein	6	Homo sapiens	P18754 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6DUB_1 Alpha N-terminal protein methyltransferase 1B (chains A, B)
GTSQVINGEMQFYARAKLFYQEVPATEEGMMGNFIELSSPDIQASQKFLRKFVGGPGRAG
TDCALDCGSGIGRVSKHVLLPVFNSVELVDMMESFLLEAQNYLQVKGDKVESYHCYSLQE
FTPPFRRYDVIWIQWVSGHLTDKDLLAFLSRCRDGLKENGIIILKDNVAREGCILDLSDS
SVTRDMDILRSLIRKSGLVVLGQEKQDGFPEQCIPVWMFALH

Sequence of entity 2 (E, F), FASTA

>6DUB_2 RCC1 (chains E, F)
XPKRIA

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Water and common crystallization additives (GOL, UNX) are not listed.

Primary citation

An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Dong, C., Dong, G., Li, L. et al. Commun Biol (2018) 1:183-183. DOI 10.1038/s42003-018-0196-2 · PubMed

Other PDB entries of the same protein (UniProt Q5VVY1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KDS 1.84 Å, Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A…
5UBB 2.0 Å, Crystal structure of human alpha N-terminal protein methyltransferase 1B
6KDR 2.11 Å, Crystal structure of human NRMT2 in complex with human centromere protein B peptide

Browse structure collections

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